**Identification of Novel Interspersed DNA Repetitive Elements in the** *Trypanosoma cruzi* **Genome Associated with the 3**′**UTRs of Surface Multigenic Families**

**Simone Guedes Calderano 1,2,\* ,**† **, Milton Yutaka Nishiyama Junior 2,3,**† **, Marjorie Marini 4,5 , Nathan de Oliveira Nunes 2,3, Marcelo da Silva Reis 2,6 , José Salvatore Leister Patané 2,6 , José Franco da Silveira <sup>4</sup> , Julia Pinheiro Chagas da Cunha 2,6 and Maria Carolina Elias 2,6,\***


Received: 8 September 2020; Accepted: 14 October 2020; Published: 21 October 2020

**Abstract:** *Trypanosoma cruzi* is the etiological agent of Chagas disease, which affects millions of people in Latin America. No transcriptional control of gene expression has been demonstrated in this organism, and 50% of its genome consists of repetitive elements and members of multigenic families. In this study, we applied a novel bioinformatics approach to predict new repetitive elements in the genome sequence of *T. cruzi*. A new repetitive sequence measuring 241 nt was identified and found to be interspersed along the genome sequence from strains of different DTUs. This new repeat was mostly on intergenic regions, and upstream and downstream regions of the 241 nt repeat were enriched in surface protein genes. RNAseq analysis revealed that the repeat was part of processed mRNAs and was predominantly found in the 3′ untranslated regions (UTRs) of genes of multigenic families encoding surface proteins. Moreover, we detected a correlation between the presence of the repeat in the 3′UTR of multigenic family genes and the level of differential expression of these genes when comparing epimastigote and trypomastigote transcriptomes. These data suggest that this sequence plays a role in the posttranscriptional regulation of the expression of multigenic families.

**Keywords:** *Trypanosoma cruzi*; genome; repeats; 3′UTR; multigenic family
